Mercurial > repos > dfornika > snippy
changeset 25:ae9dffe91f20 draft
planemo upload commit 976a7fd83686e1fe0e4ca2ee9b7c98fff7241d6d-dirty
author | dfornika |
---|---|
date | Tue, 18 Jun 2019 16:08:43 -0400 |
parents | 542d3c3d5a6e |
children | 15d5dd95daf2 |
files | snippy-core.xml snippy.xml test-data/a.dat test-data/a.tgz test-data/b.dat test-data/b.tgz test-data/c.dat test-data/c.tgz |
diffstat | 8 files changed, 22 insertions(+), 23 deletions(-) [+] |
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--- a/snippy-core.xml Mon Jun 17 16:50:34 2019 -0400 +++ b/snippy-core.xml Tue Jun 18 16:08:43 2019 -0400 @@ -45,7 +45,7 @@ <tests> <test><!-- Test #1 - test with 3 zipped directories --> - <param name="indirs" value="a.dat,b.dat,c.dat" /> + <param name="indirs" value="a.tgz,b.tgz,c.tgz" /> <param name="ref" value="reference.fasta" /> <param name="outputs" value="outtxt" /> <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
--- a/snippy.xml Mon Jun 17 16:50:34 2019 -0400 +++ b/snippy.xml Tue Jun 18 16:08:43 2019 -0400 @@ -10,6 +10,17 @@ <command detect_errors="exit_code"><![CDATA[ + #import re + #if str( $fastq_input.fastq_input_selector ) == "paired" + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier) + #elif str( $fastq_input.fastq_input_selector ) == "paired_collection" + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name) + #elif str( $fastq_input.fastq_input_selector ) == "single" + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier) + #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier) + #end if + #if $ref.is_of_type("fasta") cp '$ref' 'ref.fna' && #end if @@ -17,7 +28,7 @@ cp '$ref' 'ref.gbk' && #end if snippy - --outdir 'out' + --outdir '$dir_name' --cpus \${GALAXY_SLOTS:-1} --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024)) #if $ref.is_of_type("fasta") @@ -51,18 +62,6 @@ && - #import re - #if str( $fastq_input.fastq_input_selector ) == "paired" - #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier) - #elif str( $fastq_input.fastq_input_selector ) == "paired_collection" - #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name) - #elif str( $fastq_input.fastq_input_selector ) == "single" - #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier) - #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" - #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier) - #end if - - mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ && tar -czf out.tgz ${dir_name} #if "outcon" in str($outputs) and $adv.rename_cons && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa @@ -124,31 +123,31 @@ <outputs> - <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf"> + <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="${dir_name}/snps.vcf"> <filter>outputs and 'outvcf' in outputs</filter> </data> - <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff"> + <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="${dir_name}/snps.gff"> <filter>outputs and 'outgff' in outputs</filter> </data> - <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab"> + <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="${dir_name}/snps.tab"> <filter>outputs and 'outtab' in outputs</filter> </data> - <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt"> + <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="${dir_name}/snps.txt"> <filter>outputs and 'outsum' in outputs</filter> </data> - <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"> + <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="${dir_name}/snps.log"> <filter>outputs and 'outlog' in outputs</filter> </data> - <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa"> + <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="${dir_name}/snps.aligned.fa"> <filter>outputs and 'outaln' in outputs</filter> </data> - <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"> + <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="${dir_name}/snps.consensus.fa"> <filter>outputs and 'outcon' in outputs</filter> </data> - <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"> + <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="${dir_name}/snps.depth"> <filter>outputs and 'outdep' in outputs</filter> </data> - <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam"> + <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="${dir_name}/snps.bam"> <filter>outputs and 'outbam' in outputs</filter> </data> <data format="tar" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">